service-flask-thermorawfileparser-openms

A simple HTML interface for converting RAW format to MzML, MzXML, and MGF files.

Install

python3 -m venv env
. env/bin/activate
pip3 install flask docker python-dotenv flask-session cachelib python-memcached

Configuration

Edit .flaskenv to configure the Flask environment variables.

production

FLASK_APP = app
FLASK_DEBUG = False
FLASK_TESTING = False
FLASK_RUN_HOST="0.0.0.0"
FLASK_RUN_PORT="80"
FLASK_ENV=production

Run service

. .venv/bin/activate
flask run

production

sudo su root

python3 -m venv env
. env/bin/activate
pip3 install flask docker python-dotenv

nohup flask run > log.txt 2>&1 &

Visit http://{host}:{port}/ to access the service.

Docker images

inraep2m2/Dockerfile_thermorawfileparser

version : ThermoRawFileParser1.4.3.zip

Build and push image

docker build . -f Dockerfile_thermorawfileparser -t inraep2m2/thermorawfileparser:1.4.3
docker login --username=p2m2
docker image push inraep2m2/thermorawfileparser:1.4.3

Usage

raw data is localized in $PWD/data directory
docker run -v $PWD/data:/data -t inraep2m2/thermorawfileparser:1.4.3 -i=/data/MM_NOx_1_Direct.raw

inraep2m2/openms

Original Dockerfile

Build and push image

docker build . -f Dockerfile_openms -t inraep2m2/openms:3.1.0-pre-nightly-2024-02-03
docker login --username=p2m2
docker image push inraep2m2/openms:3.1.0-pre-nightly-2024-02-03

Usage

raw data is localized in $PWD/data directory
docker run -v $PWD/data:/data -it inraep2m2/openms:3.1.0-pre-nightly-2024-02-03 FileConverter -in /data/MM_NOx_1_Direct.mzML -out /data/MM_NOx_1_Direct.mzXML